Locus 1083

Sequence ID	X_DroMel_CAF1
Location	3,194,034 – 3,194,136
Length	102
Max. P	0.679169

overview

Window 4

Location	3,194,034 – 3,194,136
Length	102
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.40
Mean single sequence MFE	-26.00
Consensus MFE	-19.31
Energy contribution	-19.12
Covariance contribution	-0.19
Combinations/Pair	1.10
Mean z-score	-1.12
Structure conservation index	0.74
SVM decision value	0.30
SVM RNA-class probability	0.679169
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3194034 102 + 22224390
GCGGGGCGCUGUUCGCCGCUUGCAUACACGAUGUUGAUCAUCCCGGCUUAACCAAUCAGUUCUUGGUUAACUCAAGUGCGU----AUUACCU--ACA--CUUUAGUUCGU
..((((((.....))))....((((....((((.....))))..(..((((((((.......))))))))..)..))))..----....)).--...--........... ( -22.70)
>DroVir_CAF1 5676 99 + 1
GCGGGGCGCUGUUCGCUGCUUGUAUACACGAUGUUGAUCAUCCUGGUUUAACCAAUCAAUUCUUGGUUAAUUCAAGUGAGU----AACAGAA--AUA--C--CU-UUAAA
..(((...(((((.((((((((....((.((((.....)))).))..((((((((.......))))))))..))))).)))----)))))..--...--)--))-..... ( -24.80)
>DroPse_CAF1 4991 96 + 1
GCGGGGCACUGUUUGCCGCUUGCAUACACGAUGUUGAUCAUCCAGGAUUAACCAAUCAGUUUUUGGUUAACUCAAGUGAGU----AUCUCUC----------CUGGUAUU
((((((((.....)))).).)))((((..((((.....))))(((((.(((((((.......)))))))((((....))))----.....))----------))))))). ( -28.80)
>DroGri_CAF1 4395 101 + 1
GCGGGGCCCUGUUCGCCGCUUGUAUUCACGAUGUUGAUCAUCCUGGCUUAACCAAUCAGUUUUUGGUUAAUUCAAGUACGAACGAAACACAA--ACA------U-UUCAA
((((.(.......).))))(((((((...((((.....)))).((..((((((((.......))))))))..)))))))))..((((.....--...------)-))).. ( -23.00)
>DroWil_CAF1 4128 106 + 1
GCGGUGCAUUGUUCGCCGCUUGUAUACACGAUGUUGAUCAUCCUGGCUUAACCAAUCAGUUUUUGGUUAACUCAAGUGAGU----CUUUUGCGUACAGACAGCAAAUCGA
((((((.......))))))((((((.((.((((.....)))).))((.(((((((.......)))))))((((....))))----.....))))))))............ ( -27.90)
>DroPer_CAF1 5125 96 + 1
GCGGGGCACUGUUUGCCGCUUGCAUACACGAUGUUGAUCAUCCAGGAUUAACCAAUCAGUUUUUGGUUAACUCAAGUGAGU----AUCUCUC----------CUGGUAUU
((((((((.....)))).).)))((((..((((.....))))(((((.(((((((.......)))))))((((....))))----.....))----------))))))). ( -28.80)
>consensus
GCGGGGCACUGUUCGCCGCUUGCAUACACGAUGUUGAUCAUCCUGGCUUAACCAAUCAGUUUUUGGUUAACUCAAGUGAGU____AUCACAC__ACA_____CUGUUAAA
((((.(.......).)))).......(((((((.....))))..(..((((((((.......))))))))..)..)))................................ (-19.31 = -19.12 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	3,194,034 – 3,194,136
Length	102
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.40
Mean single sequence MFE	-26.02
Consensus MFE	-15.63
Energy contribution	-16.05
Covariance contribution	0.42
Combinations/Pair	1.14
Mean z-score	-1.47
Structure conservation index	0.60
SVM decision value	0.02
SVM RNA-class probability	0.544692
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3194034 102 - 22224390
ACGAACUAAAG--UGU--AGGUAAU----ACGCACUUGAGUUAACCAAGAACUGAUUGGUUAAGCCGGGAUGAUCAACAUCGUGUAUGCAAGCGGCGAACAGCGCCCCGC
.((........--.((--..(((.(----((((.((((..((((((((.......))))))))..))))..(((....)))))))))))..))((((.....)))).)). ( -25.80)
>DroVir_CAF1 5676 99 - 1
UUUAA-AG--G--UAU--UUCUGUU----ACUCACUUGAAUUAACCAAGAAUUGAUUGGUUAAACCAGGAUGAUCAACAUCGUGUAUACAAGCAGCGAACAGCGCCCCGC
.....-.(--(--(..--..(((((----.....((((..((((((((.......))))))))..((.((((.....)))).))....)))).....))))).))).... ( -22.60)
>DroPse_CAF1 4991 96 - 1
AAUACCAG----------GAGAGAU----ACUCACUUGAGUUAACCAAAAACUGAUUGGUUAAUCCUGGAUGAUCAACAUCGUGUAUGCAAGCGGCAAACAGUGCCCCGC
....((((----------((.....----((((....))))(((((((.......))))))).))))))(((((....)))))........(.((((.....)))).).. ( -25.40)
>DroGri_CAF1 4395 101 - 1
UUGAA-A------UGU--UUGUGUUUCGUUCGUACUUGAAUUAACCAAAAACUGAUUGGUUAAGCCAGGAUGAUCAACAUCGUGAAUACAAGCGGCGAACAGGGCCCCGC
.....-.------.((--((((((((((.((((.((((..((((((((.......))))))))..)))))))).......)).))))))))))(((.......))).... ( -27.60)
>DroWil_CAF1 4128 106 - 1
UCGAUUUGCUGUCUGUACGCAAAAG----ACUCACUUGAGUUAACCAAAAACUGAUUGGUUAAGCCAGGAUGAUCAACAUCGUGUAUACAAGCGGCGAACAAUGCACCGC
..(.(((((((..((((..((...(----(.(((((((..((((((((.......))))))))..)))).))))).......))..))))..)))))))).......... ( -29.30)
>DroPer_CAF1 5125 96 - 1
AAUACCAG----------GAGAGAU----ACUCACUUGAGUUAACCAAAAACUGAUUGGUUAAUCCUGGAUGAUCAACAUCGUGUAUGCAAGCGGCAAACAGUGCCCCGC
....((((----------((.....----((((....))))(((((((.......))))))).))))))(((((....)))))........(.((((.....)))).).. ( -25.40)
>consensus
AAGAACAG_____UGU__GAGAGAU____ACUCACUUGAGUUAACCAAAAACUGAUUGGUUAAGCCAGGAUGAUCAACAUCGUGUAUACAAGCGGCGAACAGUGCCCCGC
..................................((((..((((((((.......))))))))..((.((((.....)))).))....)))).((((.....)))).... (-15.63 = -16.05 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:07 2006